AMBER Archive (2002)

Subject: RE: entropy calculation

From: case (case_at_scripps.edu)
Date: Tue Jun 11 2002 - 08:56:37 CDT

>===== Original Message From "X. Tan" <xjtan_at_u.washington.edu> =====

>when I ran mm_pbsa, I got stucked in the nmode calculation. I have some
>questions about it.
>
>1. can I just calculated residues 8 A (or less)around the ligand? and is
>that enough to give out the correct answer?

No.

>
>2. I need to do nmdoe calculations for complex, protein and ligand for
>each snapshot or only one set?

One is the minimum; may people would evaluate five snapshots or so, to
see how the entropy estimate varies.

..good luck...dac

==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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